Generates the 2D coordinates of a molecule by maximizing its overlay
with a reference 2D molecule based on multiple overlaps between the
two molecules.

fitmol

The molecule being fitted to be aligned to the reference molecule.

refmol

The reference molecule of which 2D coordinates are remain unchanged.

miter

The iterator that stores the matches on which the molecule
alignment is based on.

Example of the molecule alignment based on multiple fragments

(left) - depiction of a reference molecule
(middle) - default depiction of a fit molecule
(right) - depiction of the fit molecule aligned to the reference based on multiple fragments

Hint

The overlap between two molecules can be generated by the
OEGetFPOverlap function of Graphsim TK.
The OEGetFPOverlap returns matched fragments
of two molecules that are considered equivalent based on a specific
fingerprint type.

The Python script that visualizes molecule similarity based on fingerprints
can be downloaded from the
OpenEye Python Cookbook